Variant report

Variant	rs12665641
Chromosome Location	chr6:25519901-25519902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1022492	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10946784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12663643	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13192159	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs16890653	0.83[EUR][1000 genomes]
rs2049967	0.84[GIH][hapmap];0.87[TSI][hapmap]
rs2072848	0.91[ASN][1000 genomes]
rs2072849	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs212934	0.82[CHB][hapmap]
rs2205935	0.84[TSI][hapmap]
rs2272824	0.84[ASW][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap]
rs3747526	0.84[ASW][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap]
rs3804120	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs3804123	0.91[JPT][hapmap]
rs3804124	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3804125	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3804126	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3804127	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3827505	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6935799	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7738571	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7740510	0.83[GIH][hapmap]
rs7760799	0.86[EUR][1000 genomes]
rs7767930	0.84[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs7776417	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9295665	0.91[CHB][hapmap];0.93[YRI][hapmap]
rs9348683	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9356979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356980	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9356981	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9356983	0.86[ASN][1000 genomes]
rs9358859	0.86[EUR][1000 genomes]
rs9366625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379771	0.87[CHB][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379772	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9393647	0.86[EUR][1000 genomes]
rs9393648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9393649	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12665641	TRIM38	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25456400-25537000	Weak transcription	Esophagus	oesophagus
2	chr6:25463200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:25471600-25597200	Weak transcription	Gastric	stomach
4	chr6:25480800-25523600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:25483000-25532200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:25490400-25521800	Weak transcription	GM12878-XiMat	blood
7	chr6:25490400-25543000	Weak transcription	Hela-S3	cervix
8	chr6:25490600-25524600	Weak transcription	A549	lung
9	chr6:25490800-25521400	Weak transcription	Small Intestine	intestine
10	chr6:25491600-25521000	Weak transcription	HSMMtube	muscle
11	chr6:25494000-25551400	Weak transcription	Left Ventricle	heart
12	chr6:25500600-25520800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:25500600-25523800	Weak transcription	Placenta	Placenta
14	chr6:25506600-25537400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:25506800-25521000	Weak transcription	NHEK	skin
16	chr6:25507600-25525600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:25508800-25521200	Weak transcription	Spleen	Spleen
18	chr6:25509800-25548600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:25511600-25522800	Weak transcription	Primary B cells from cord blood	blood
20	chr6:25511600-25531400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:25512200-25525600	Weak transcription	NHLF	lung
22	chr6:25512800-25521800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:25513800-25524400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:25513800-25530200	Weak transcription	Brain Germinal Matrix	brain
25	chr6:25514000-25525600	Strong transcription	Primary T cells from cord blood	blood
26	chr6:25514200-25542600	Weak transcription	Adipose Nuclei	Adipose
27	chr6:25514200-25558400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:25514400-25523000	Weak transcription	Brain Angular Gyrus	brain
29	chr6:25514400-25541600	Weak transcription	Colonic Mucosa	Colon
30	chr6:25514600-25523800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:25514800-25537800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr6:25515000-25538600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:25515200-25522000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr6:25515400-25525000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr6:25515600-25523000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr6:25515600-25525600	Strong transcription	Fetal Thymus	thymus
37	chr6:25515800-25521400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:25515800-25522600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:25515800-25523200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:25515800-25523400	Strong transcription	Fetal Intestine Large	intestine
41	chr6:25516000-25524200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:25516200-25520600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr6:25516200-25547000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:25516200-25556800	Weak transcription	Pancreas	Pancrea
45	chr6:25516400-25521000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:25516400-25521200	Weak transcription	Brain Anterior Caudate	brain
47	chr6:25516400-25523600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:25516400-25556800	Weak transcription	Fetal Stomach	stomach
49	chr6:25516600-25520800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:25516600-25539600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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